Our goal is to fit the multiple instances (or structures) of a generic model existing in data. Here we propose a novel model selection scheme to estimate the number of genuine structures present. In contrast to conventional model selection approaches, our method is driven by kernel-based learning. The input data is first clustered based on their potential to have emerged from the same structure. However the number of clusters is deliberately overestimated to obtain a set of initial model fits onto the data. We then resolve the oversegmentation via a series of kernel optimisation conducted through multiple kernel learning, and the concept of kernel-target alignment is used as a model selection criterion. Experiments on synthetic and real data show that our method outperforms previous model selection schemes. We also focus on the application of multi-body motion segmentation. In particular we demonstrate success on estimating the number of motions on sequences with more than 3 unique motions.